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- PDB-6sup: Crystal Structure of TcdB2-TccC3-Cdc42 -

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Basic information

Entry
Database: PDB / ID: 6sup
TitleCrystal Structure of TcdB2-TccC3-Cdc42
ComponentsTcdB2,TccC3,Cell division control protein 42 homolog
KeywordsTOXIN / Toxins / Tc Toxins
Function / homology
Function and homology information


GBD domain binding / positive regulation of pinocytosis / COG complex / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / embryonic heart tube development ...GBD domain binding / positive regulation of pinocytosis / COG complex / storage vacuole / cardiac neural crest cell migration involved in outflow tract morphogenesis / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / regulation of attachment of spindle microtubules to kinetochore / organelle transport along microtubule / embryonic heart tube development / endothelin receptor signaling pathway / Inactivation of CDC42 and RAC1 / positive regulation of pseudopodium assembly / host-mediated perturbation of viral process / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / establishment of Golgi localization / dendritic spine morphogenesis / establishment of epithelial cell apical/basal polarity / cell junction assembly / GTP-dependent protein binding / heart process / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / RHO GTPases activate KTN1 / DCC mediated attractive signaling / positive regulation of filopodium assembly / CD28 dependent Vav1 pathway / regulation of postsynapse organization / Wnt signaling pathway, planar cell polarity pathway / phagocytosis, engulfment / RHOV GTPase cycle / Myogenesis / establishment of cell polarity / small GTPase-mediated signal transduction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / RHOQ GTPase cycle / Golgi organization / RHOU GTPase cycle / macrophage differentiation / establishment or maintenance of cell polarity / CDC42 GTPase cycle / RHO GTPases activate PAKs / RHOG GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / negative regulation of protein-containing complex assembly / RHO GTPases activate IQGAPs / GPVI-mediated activation cascade / RAC1 GTPase cycle / phagocytic vesicle / EPHB-mediated forward signaling / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / integrin-mediated signaling pathway / actin filament organization / regulation of actin cytoskeleton organization / small monomeric GTPase / FCGR3A-mediated phagocytosis / filopodium / EGFR downregulation / RHO GTPases Activate Formins / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / mitotic spindle / endocytosis / MAPK6/MAPK4 signaling / cytoplasmic ribonucleoprotein granule / apical part of cell / microtubule cytoskeleton / cell-cell junction / actin cytoskeleton organization / G beta:gamma signalling through CDC42 / ubiquitin protein ligase activity / positive regulation of cell growth / Factors involved in megakaryocyte development and platelet production / G protein activity / midbody / postsynapse / neuron projection / positive regulation of cell migration / Golgi membrane / focal adhesion / neuronal cell body / centrosome / GTPase activity / dendrite / protein kinase binding / endoplasmic reticulum membrane / GTP binding / glutamatergic synapse / signal transduction
Similarity search - Function
Shell / RHS repeat-associated core / RHS repeat-associated core / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat ...Shell / RHS repeat-associated core / RHS repeat-associated core / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Cdc42 / : / Rhs repeat-associated core / Small GTPase Rho / Small GTPase Rho domain profile. / Integrin alpha, N-terminal / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog / TccC3 / TcdB2
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRoderer, D. / Schubert, E. / Sitsel, O. / Raunser, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Nat Commun / Year: 2019
Title: Towards the application of Tc toxins as a universal protein translocation system.
Authors: Daniel Roderer / Evelyn Schubert / Oleg Sitsel / Stefan Raunser /
Abstract: Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that ...Tc toxins are bacterial protein complexes that inject cytotoxic enzymes into target cells using a syringe-like mechanism. Tc toxins are composed of a membrane translocator and a cocoon that encapsulates a toxic enzyme. The toxic enzyme varies between Tc toxins from different species and is not conserved. Here, we investigate whether the toxic enzyme can be replaced by other small proteins of different origin and properties, namely Cdc42, herpes simplex virus ICP47, Arabidopsis thaliana iLOV, Escherichia coli DHFR, Ras-binding domain of CRAF kinase, and TEV protease. Using a combination of electron microscopy, X-ray crystallography and in vitro translocation assays, we demonstrate that it is possible to turn Tc toxins into customizable molecular syringes for delivering proteins of interest across membranes. We also infer the guidelines that protein cargos must obey in terms of size, charge, and fold in order to apply Tc toxins as a universal protein translocation system.
History
DepositionSep 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TcdB2,TccC3,Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,9034
Polymers240,8311
Non-polymers733
Water23,0411279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-25 kcal/mol
Surface area86710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.350, 156.550, 179.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TcdB2,TccC3,Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 240830.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus luminescens (bacteria), (gene. exp.) Homo sapiens (human)
Gene: tcdB2, TccC3, CDC42 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GF99, UniProt: Q8GF97, UniProt: P60953, small monomeric GTPase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium chloride, 0.1 M magnesium chloride, 0.1 M tri-sodium citrate pH 5.5, 12 % PEG 4000 Seeding: 0.1 M magnesium chloride, 0.1 M tri-sodium acetate pH 4.6, 12 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97958 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→48.17 Å / Num. obs: 182401 / % possible obs: 99.9 % / Redundancy: 22 % / CC1/2: 0.998 / Net I/σ(I): 13.81
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1.46 / Num. unique obs: 18014 / CC1/2: 0.688

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XSCALEVERSION Mar 15, 2019 BUILT=20190315data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9X

4o9x


Resolution: 2→48.17 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.32 --
Rwork0.287 --
obs-182143 99.5 %
Refinement stepCycle: LAST / Resolution: 2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17002 0 3 1282 18287

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